     (event-fn)))
 
 (defn stop-acq []
-  (dosync alter state assoc-in [:interrupt-requests :stop] true))
+  (dosync (alter state assoc :stop true)))
   
 (defn pause-acq []
-  (dosync alter state assoc-in [:interrupt-requests :pause] true))
+  (dosync (alter state assoc :pause true)))
   
 (defn run-acquisition [settings out-queue] 
   (def acq-settings settings)
   (binding
-    [state (ref {:interrupt-requests {:pause false :stop false}
+    [state (ref {:pause false
+                 :stop false
                  :z-corrections nil
                  :last-wake-time (clock-ms)
                  :start-time (clock-ms)

(defn set-stage-position
  ([stage-dev z] (log "setting z position to " z)
		 (core setPosition stage-dev z)
		 (dosync alter state assoc :last-z-position z))
  ([stage-dev x y] (log "setting x,y position to " x "," y)
                   (when (and x y) (core setXYPosition stage-dev x y))))



(ns org.micromanager.acq-engine
  (:use [org.micromanager.mm :only [when-lets map-config get-config get-positions 
                                    get-default-devices core log log-cmd mmc gui with-core-setting]]
        [org.micromanager.sequence-generator :only [generate-acq-sequence]])
  (:import [org.micromanager AcqControlDlg]
           [org.micromanager.api AcquisitionEngine]
